The dataset contains dissolved nutrient concentrations from water samples collected during a 16-day in-situ incubation experiment in the Baltic Sea (2025-07-12 to 2025-07-29). Samples were collected using an automated glass-syringe sampler deployed within two benthic chambers of a Biogeochemical Observatory (BIGO, Sommer et al., 2009) at 54° 34.432' N, 10° 10.776' E, at 22 m water depth. In one chamber, 29 g of fine calcite powder were added to the bottom water as part of an enhanced benthic calcite weathering experiment. Seven samples per chamber and from the ambient bottom water were analyzed to assess potential nutrient fluxes associated with the calcite addition and benthic biogeochemical processes.